The Scattered Leaves
by Alpha Cyborg J
Summary: A man with a dream is a man not easily swayed. Pain is not moved by Naruto's words and so Naruto must make a choice. A choice that will change the fate of Konoha and the Elemental Nations as a whole. Canon compliant up to Pain's assault on Konoha. No mass revival. Pairings undecided (If any).
1. A Steadfast Will

**Prologue**

 **A Steadfast Will**

 _This boy,_ Nagato thought to himself as he digested the words that had just been spoken to him. He was at war with himself thanks to this boy, his brother disciple. But he knew deep down what his answer would be. Every fiber of his being pulled him towards believing in him and for a moment he was ready to do just that, but two things stopped him. Fear of Naruto's failure to bring peace and his own memories and regrets.

Nagato looked at Naruto with what could be considered a look of regret, before saying "I'm sorry, but your words have not moved me. You're too young, too naive and too inexperienced. You may have experienced pain and hardship but you haven't truly had time to reflect on that nor have you seen what the world is _truly_ like. I cannot place my faith in you, not after all the sacrifices that have been made and especially not when you don't even have a plan on making true peace possible"

Naruto couldn't believe what he was hearing. Even after defeating him and all his efforts to get through to him Nagato still wouldn't be swayed. "Please, you have to trust me, I may not have a plan yet but that doesn't mean I can't do it. You said the same thing about me beating you and look what happened. Just...just at least let me try." Even though he had won Naruto didn't want Nagato as an enemy, not after hearing his story and he didn't want to kill him either. Not like this.

"I wish I could...but the world doesn't work like that. I can't give you my blessings when you plan to merely wing it. Improvisation and luck only go so far. The same could be said about our fight. Your victory was equal parts power and luck. Had I been trying to kill you rather than capture or had your friend not interfered you would not be standing here right now. Also...I can't give up, not after coming this far...not after all the sacrifices that have made for the sake of peace."

Naruto stood in silence at his response before clenching his fists and saying, "All the sacrifices huh? What about Ero-sennin, what about Konoha!? Were they for the sake of peace too? Tell me how their deaths were for peace!"

Nagato closed his eyes and said "Jiraiya sensei's death was regrettable but it was necessary. I will be honest with you though, Konoha's destruction wasn't for peace's sake, it was for mine. After all the things Konoha has done to me I couldn't just let that go. I'm not like you, not anymore."

Naruto didn't have a response to that. He knew what Konoha had done to him, though he also knew what Ero-sennin had done for him but he knew saying that wouldn't change his mind. "Fine, what happens now?" he says, defeated.

"That's up to you. I'm not in a position to stop you from doing anything." said Nagato causing Konan to shift from her until then silent vigil. "Nagato-" she starts.

"No Konan, I lost this battle. Whatever happens, don't interfere." says Nagato. He didn't want Konan to fight Naruto. He may have gotten lucky but he was still strong enough to beat his paths. He didn't want to lose Konan either, losing Yahiko was enough and he'd rather die than lose her too.

"What are you gonna do when you get out here?" asks Naruto.

Nagato knew the smart thing to do was to reassure Naruto that he'd stop his machinations but he felt he at least owed it to him to be honest about his intentions. "I'm going to continue working towards peace. Like I said before, I've already come too far to give up."

He was afraid of that answer, after all the damage that Nagato had done he couldn't just let him go. He was simply too powerful for that. As much as Naruto hated to admit it, he DID get lucky in this fight and he wasn't sure he could do it again. He figured that given enough time he could refine sage mode and his other techniques but he didn't know how much time he'd get. He had no idea how long it would take before Nagato recovered his fighting strength and attacked again. Konoha was already in ruins and he knew if Nagato attacked again it'd be finished if it wasn't already.

"I can't just let you go y'know? Not if you're gonna come back." Naruto said softly.

"Then do what you have to do. Because I will never give up, a sentiment I'm sure you know well." said Nagato with an edge of steel to his tone.

Naruto looked at Nagato with no small amount of hesitation. He was unsure of what to do. He didn't want to kill Nagato but the Rinnegan was just too powerful and he couldn't let him destroy what was left of Konoha. _That's it!_ He thought to himself, having thought of the solution to this. What he was about to do almost made him sick but it was better than just killing him and with a look of determination he began to walk towards him.

Seeing this Konan began to move as well but Nagato shook his head and she gritted her teeth and stepped back, worry clearly shown on her face.

When Naruto finally closed the distance he said to Nagato "I'm sorry" and that's when he acted.  
With a single swift slash he ran his kunai across Nagato's face, destroying the only pair of Rinnegan currently in existence.

Nagato was prepared for death. He had been prepared for it the moment Naruto defeated Deva path. What he was not prepared for was this. So shocked that he was he couldn't contain his shout of pain and confusion. Gone were his divine and blessed eyes and replaced with pain and darkness. _This is his solution? It would have been kinder to kill me._ He thought to himself.

Seeing the blood pouring from the remains of Nagato's eyes was horrifying but he couldn't look away. He couldn't believe he had actually done that and felt disgusted with himself. Then he remembered what Konoha had looked like when he arrived, he remembered Hinata's face and confession...before Pain killed her, he remembered the time he had spent with Jiraiya and he didn't want to lose anything else to this man. "I didn't want things to end like this but I am a Konoha shinobi and I'll do what's best for it...I hope the next time we see each other you'll have changed your views. Goodbye."

Naruto begins to leave, wanting to leave this behind him but Konan materializes in front of him in a flurry of origami paper. "Do you really think I'll just let you leave after doing that!?" she says in an icily yet evidently angry voice.

Naruto sighs and prepares himself for the battle that is to come. He really didn't want things to end like this. Before either of them makes a move Nagato speaks up and says "Konan, let him go. It's over."

She gives Naruto an icy glare but reluctantly steps aside letting him pass. As Naruto begins his trek back to the remains of Konoha, there's only one thing going through his mind. _What the hell are we going to do now?_

* * *

 **This is a very short chapter but that is because it's a prologue. I can promise you that all subsequent ones will be longer. As my first written fanfic any feedback is welcome. Either positive or negative.**


	2. The Last Bastion

**Chapter 2**

 **The Last Bastion**

Danzo was irritated. Never before had Konoha been in such a state and to make matters worse the perpetrator was someone he knew. Someone that should have been dead. He was brought from his musings when one of agents landed on the broken tower he taken watch on. "Report." Was all he said.

"Sir, as you well know the main infrastructure of Konoha was completely destroyed with 80% of its buildings completely destroyed and the remaining 20% heavily damaged."

As the agent said Danzo had expected this. It was plain to see with merely a glance. "And what of our casualties?"

"Our civilian casualties are only at roughly 600 with several hundred more injured, but alive. The rest had made it to the shelters before Pain's widespread jutsu."

Danzo was pleased to hear this. Unlike some shinobi, Danzo knew that civilians were just as important to the village as they were. They were what kept the village running at the administrative and economical level and if not for them shinobi would have to be dedicated to those tasks which would hurt their fighting strength, not to mention the economical ramifications of a purely shinobi village. Having over 90% of the civilian population remain was a blessing Danzo couldn't have hoped for. "And what of our shinobi." He said. Unlike the civilians, Danzo knew that the shinobi were in the thick of it and he dreaded the answer to this question.

"So far we have confirmed almost 7000 as K.I.A, including Kakashi Hatake. Another 10000 are in various states of injury but thanks to Lady Tsunade's summons they are expected to survive."

Danzo frowned at this news. 85% was a significant portion of shinobi to have out of action and 35% of them were permanently gone. There was also the fact that Hatake was lost as well. He may not have been one of Danzo's shinobi, not anymore, but he was a very valuable asset to the village. He supposed he should be grateful that it wasn't higher. He may not have respected the current Hokage much but he would give her credit where it was due. Her medical expertise was what truly saved them from being completely annihilated today. That and the Jinchuuriki.

Almost as if on cue another agent arrived and said, "Sir, Uzumaki has returned. It appears that he was victorious."

"I see. Continue to assess the situation and report to me later." Danzo says before turning away.

Seeing their dismissal, the two agents depart, leaving Danzo to his thoughts. I must bring him under my control. Now more than ever do we need to have a unified front. He thought to himself. With that final thought he left his ruined perch. He had preparations to make after all.

* * *

Naruto didn't know what to expect when he came back but he was surprised to see how many people smiled at him or gave him approving nods as he passed them but what truly surprised him was seeing Sakura standing near Hinata. After the way she was taken down he didn't think she'd survive. Not something like that. He was broken out of his thoughts by Sakura running towards him and throwing her arms around him.

"You idiot…how could you be so rash?" she says in tears. "Thank you." She amends, knowing that it's thanks to him that Konoha was saved, that she was saved.

Naruto doesn't quite know what to say to this or to the others he could hear in the background calling him a hero. He didn't quite know if that was accurate. He may have stopped Pain…no, Nagato but he still was too late to stop him from doing so much damage. He needed to become stronger and he needed to become faster. He couldn't afford to be late ever again and now knowing just who his father was he had just the idea on how to accomplish that. "Sorry Sakura, I didn't mean to make you worry." He says.

"No, forget I said that. I should know by now that you'll always pull through. It's what you do. Next time though, I want to be there when you do." She says determined to catch up to him. She thought she had closed the gap between them after all these years but she sees now that she still has far to go before she could stand side by side with him. But for his sake and for the sake of Konoha she'd do just that. She wouldn't be spectator waiting to be saved, again.

"I look forward to it. So…now that the fight's over what's happening now?" Naruto asks.

"I'm unsure…Before you came back Tsunade-sama fell into a coma from using Katsuya and Sōzō Saisei to save the villagers so I don't know what's going to happen now, especially since Kakashi-sensei's…" She's unable to finish that sentence before she tries and fails to fight back tears.

The reality of the current situation came crashing back onto Naruto and he too had to fight his tears back. He suspected that that was the case with Kakashi-sensei when Tsunade remained silent when he asked about him but some part of him remained hopeful that he just was unconscious and he couldn't sense him. "Oh..." was all he could get out.

Seeing their downcast states several villagers try to raise to raise their spirits but given that they too are suffering from the loss of the village it's all rather halfhearted. For Naruto and all of Konoha this was only a victory in the barest sense of the word. To them they merely survived.

* * *

Danzo couldn't believe how lucky they had gotten, all things considered. Despite the devastation that had brought upon Konoha all of the major clan heads, and the two other Hokage advisors had survived. The last thing Konoha needed was broken leadership. The Hokage being out of commission was advantageous to him but anything more would be a hindrance.

"So, does anyone have any suggestions about what we're going to do to resolve this crisis?" Asked Chouza, trying to keep the pain out of his voice. He may be alive but he didn't have any illusions about the fact that he could very well be one of the dead right now.

"I believe we should take stock of the situation before taking any hasty actions." Said Inoichi.

A few of the other clan heads nodded in approval. That was clearly the sensible option.

"Is that what you think we should do? Do you really think we should sit around and wait for our enemies to discover our situation and take advantage of it?" Says Danzo.

"Well what do you suggest then? Huh? You got some grand plan to make this right?" exclaims an annoyed Tsume.

Danzo inwardly smiles to himself, glad that he was given the opportunity to propose his plan. "I propose that we regroup in Toride Tower." Danzo waited for the expected outrage and was not disappointed.

"What? Have you lost your mind?" exclaims Inoichi with the other council members expressing similar thoughts at the idea. Even Homura and Koharu looked uneasy at the idea.

"You do realize that's in the center of the Forest of Death right?" says Tsume in a patronizing tone.

"Hmph. What you all fail to realize is that this is what Toride Tower's very purpose is. What you may not know is that during the First Shinobi War It was built as a fallback point in the event that the village was overrun. But I suppose only myself and my teammates would know about that." Says Danzo.

"Even if that were the case how do you intend on falling back there? It's one thing for the shinobi but getting the civilians there is an entirely different matter. Not mention that there's no way a single tower can accommodate the entirety of our population." Says Hiashi.

"There is more to Toride Tower than you know. On the outside it's merely a tower but it has a quite spacious subterranean level, more than enough to hold the population until proper dwellings can be built. It is also linked to an underground network that connects to the shelters within the Hokage Monument which solves the issue of getting them there. Tobirama-sensei was not so foolish as to merely build a tower in the most dangerous forest in country or perhaps even the continent and call it the main fallback point." Says Danzo, both pleased yet annoyed at how well the tower's real function has remained unknown. It's good that it has not become a well-known fact but surely the top brass should know of such a thing. If he and his teammates had died as well, Konoha would surely be floundering right now.

"And what then? You said something about proper dwellings being built. Do you intend for Konoha to be relocated there? How would that even work?" Asks a skeptical Chouza.

"Yes. It's far more secure than our village with its natural defenses and with the help of Yamato and conventional building we can build around the tower, subduing and pushing out any of the dangerous animals within the vicinity. There's an original reason that it was mandated that the three kilometers surrounding the tower were to be cleared and patrolled. It was just lost in time."

"I can see the wisdom in this. Had I known of its significance I'd have proposed a similar plan." Says Shikaku, who's been silent until then.

"Well if Shikaku is on board I can't see any reason not to as well." Says Chouza.

Inoichi could also see the wisdom in it as well but was more reluctant to agree than his former teammates. He didn't trust Danzo in the slightest but he really couldn't see any way that Danzo could use this as a power play so with a good deal of hesitance he voiced his agreement as well.

It didn't take long for the other clan heads to agree to the plan and naturally Koharu and Homura were on board from the moment Danzo proposed the plan.

"Let's get one thing straight though, Danzo. This may be your plan but that doesn't mean you're in control. I hope you remember that." Said Inoichi

Danzo couldn't help but chuckle and say "At this moment I could care less about that. So long as Konoha survives this and remains strong it doesn't matter who leads it." A lie. To Danzo, the two were intertwined. If it wasn't him who led Konoha then Konoha wouldn't be strong. It probably wouldn't survive. But he obviously couldn't share that sentiment. Not that he needed to. Once they met with the Fire Daimyo he would be in control. There were simply no candidates now that Hatake was dead. The only eligible ones were clan heads and as a rule major clan heads were only chosen if they had something really special about them as it was conflict of interest. None of the current clan heads had that. Unless Tsunade woke up, it was all but certain that Danzo would become the next Hokage. And he had half a mind to make sure she never did.

* * *

There weren't many things that could leave Tobi in stunned silence but this, this was surely one of them. "You…do you realize what you've done? You've ruined _everything!"_ He said in barely suppressed rage when he finally managed to speak.

"Madara…It's not over yet. We still have seven of the Bijuu. We can still create the Kami No Sabaki even if in a weakened state." Says Pain.

"Impossible. Without all nine it's useless and without the Rinnegan the Gedo Mazo statue can't be accessed anyways. How could you possibly have been defeated by the Kyuubi Jinchuuriki, a sixteen-year-old boy?" Tobi said. What Pain didn't know was that "Kami No Sabaki" didn't even exist. Of course it wouldn't do to tell him that.

Pain was getting angry about effectively being scolded like a child but was able to keep his cool in light of the fact that he was basically defenseless at this point and antagonizing Madara would not be wise. "I underestimated him. I had expended to much energy when destroying Konoha and he was able to capitalize on that. Between his "Sage Mode" and the powers his Bijuu gave him he was a formidable opponent. Had I been trying to kill him I'd have won but I realize now that he's not someone to hold back against."

"Excuses. You should have just killed him then. Having to wait a few months or years for the Kyuubi to reform while annoying would have been far preferable to you losing the Rinnegan." He knew that he was hurting Pain's pride by speaking to him like this but some part of him relished in it. The man deserved a reality check. Another part though, was furious. Unless he managed to acquire another Rinnegan everything they have done up until now would be nothing. Still, he had a couple ideas in regards to that but for now he was going to recover something that was long due to be in his possession. "I'm leaving. I may have a solution to this but first there's something of mine I must get back." With that he disappeared with his transportation jutsu.

"I hate that man." Said Konan. She truly did. It was because of him that the Akatsuki was corrupted into its current form.

"As do I, but for the time being he's necessary. If we wish for peace, then we have to work with unsavory characters." Said Nagato

"I know; I hope whatever his plan is it works. Otherwise…"

"Otherwise he's of no more use to us." Nagato finished. He was beginning to consider other avenues to achieve peace.

* * *

 _So this is what Pain has wrought_. Thought Tobi as he took in the destruction around him. He was willing to admit that it kind of made him a little envious. Pain did what he could not all those years ago and he did it without a Bijuu. _Still, at least my attempt didn't leave me powerless._ He could at least take solace in that fact. He stopped his musings and looked down at the body of his one-time friend.

 _Just like before you couldn't protect anything. I'll be taking back what's mine now._ And with that thought he reached down and plucked out the eye that arguably made Kakashi famous. He contemplated destroying the body to eliminate any evidence of what happened here but decided it didn't matter. It'll just hurt their morale even more when they eventually start cleaning up and find him missing his eye, he figured. Also part of him couldn't bring himself to do it, not that he acknowledged that. With his objective done his body flowed back into his personal dimension leaving no trace of his visit, aside from the desecrated corpse of his teammate of course.

* * *

Naruto was beginning to regret volunteering to help with clean up and retrieval. It's not that it was hard, at least not physically. It was just…mentally and emotionally exhausting. Many people didn't escape from Nagato's jutsu alive and finding their broken bodies was beginning to take its toll on his psyche. But Naruto knew that his contribution to this was needed. Few or perhaps no ninja could use the Kage Bunshin to the extent that he could and that made a huge difference here. There was also the fact that Naruto felt he needed to do this on a personal level. Nagato came here for him and he felt that he needed to see with his own eyes what the result of that was. What the result of him being late was. The one positive to it though was finding the survivors. Sakura and Ino were with him on this as well and quite a few people buried under the debris were saved thanks to them. So saving them made it worth it to him.

He was brought out of his thoughts when he heard a scream pierce the air. Sakura's scream. Without pause he created a clone and instructed it to start gathering nature chakra and rushed to her side. What he was expecting was another enemy, perhaps another member of Akatsuki. What he got though was somehow worse in his mind. It was Kakashi-sensei. With his eye gouged out. _Is this a message to me? For what I did to Nagato?_ He couldn't help but think that. Banishing those thoughts, he tried his best to comfort Sakura but he was just as shaken as she was. It didn't help that a crowd was starting to form.

Soon enough an ANBU operative arrived and took the body away. Naruto wanted to protest but he couldn't find any reasonable argument so he kept his silence on the matter. His mind on the other hand was all but silent. Who did this? Was it Nagato trying to replace his eye? An act of revenge towards him? Or was it someone simply taking advantage of the situation? Neither of those thoughts sat well with him nor did the rising darkness that sat beneath them. He wanted to destroy whoever did this and that's what bothered him the most.

* * *

The members of the council were visibly disturbed by the news they just received. Someone not only infiltrated Konoha but also made off with Kakashi's Sharingan. The last Sharingan in their possession. Crater or not, Konoha was still not an easy place to infiltrate.

"We need to do something about this. Until we complete the move to Toride Tower we will remain vulnerable." Said Hiashi

"Indeed. If our enemies find out that they can just come in and take what they want, we'll have Iwa and Kumo on our doorstep in no time." Said Koharu

"I may have a solution to this as well." Said Danzo.

"Really? Another idea from the old warhawk. It's like you think you're already Hokage." Said Tsume, blunt as ever.

"She may not have been very subtle about it but she does have a point. I find it very suspicious that you seem to have all the answers to our problems." Said Inoichi

"Hmph. That's because I have contingencies in place for all foreseeable scenarios, even negative ones such as this. I'm not so naïve as to wait until after the fact to react. Now if you're done trying to find some angle on me, I'd like propose my plan." Said Danzo, unphased by the opposition to him. It was nothing he wasn't used to.

"Fine, but we reserve the right to shut it down." Said Inoichi.

"Of course. I believe that we should erect a mass genjutsu around the remains of Konoha with the illusion being that it's still intact. Perhaps with some moderate damage in case someone gets wind of the fact that it was destroyed. We can pass it off as being wildly exaggerated rumors. On top of that we will bar anyone entrance from entering within ten kilometers of Konoha. Once the move to Toride Tower is complete we can remove the genjutsu and use our Doton specialists to fill the crater as it's currently a sign of weakness." Said Danzo

"That's a good plan but there's one problem with that. We don't have a genjutsu specialist who could create a jutsu of that magnitude. That's impossible." Said Chouza.

"I never said we would use one shinobi for that task. It would be a team creating this jutsu with members rotating in and out at regular intervals."

Once again Shikaku was the first to agree to the idea. "That could work. As you said it's not a permanent solution but for the time being I believe that's the best course of action."

Again, like before, the rest of the council was quick to agree to it once Shikaku did. The rest of the meeting was spent going over the specifics and preparing for the trip to Hi no Kuni's capital to consult with the Fire Daimyo.

* * *

"So, Konoha was demolished huh?" Sasuke asked in an uncaring tone.

"Yes, Pain was quite effective in that area. Even if he failed at everything else." Said Tobi

"And what of the elders? Did they die as well?" Sasuke asked. Part of him hoped they did but for the most part he wanted them to have survived. He wanted to kill them himself.

"I'm afraid not. Though I guess that means you'll still get your chance at them."

"Good." He looked at the rest of his team and said. "Get ready to leave. We're headed for Konoha."

* * *

 **AN**

 **Toride - Bastion. As far as I can tell the tower in the Forest of death doesn't have a name or real purpose in canon so I gave it one.**

 **Kami No Sabaki - God's Judgement. It's the name I've given to the weapon that Pain believes Akatsuki is creating with the Bijuu. As far as I can tell it was never given an actual name in canon.**

 **Also, if anyone knows how to center the chapter title can you please tell me. It looks centered when unpublished but just looks weird when I actually publish it.**


End file.
